BioPAX-Boston Google Group

Re: Meeting today

2007-10-31T00:29:47Z

Hi,
I need a little more notice than this :-)
I dug around and before the "meeting today" message, the last message
I saw about meeting was from Jonathan on October 2 (and I hadn't seen
that message either until today :-).
How'd it go?
Joanne
Joanne Luciano, PhD
Predictive Medicine, Inc.
45 Orchard Street

Re: Meeting today + OBO and PWpool papers

2007-10-30T15:04:17Z

Hi Oliver -
Somebody may have more recent updates, but this cites the principles:
[link]
Dan Corwin
PS - I once promised to send you a link on Pathway Pools, which is
below. I'd guess it overlaps with things that you envision -
[link]

Re: Meeting today

2007-10-30T14:40:19Z

Dear friends,
Thank you! What are BFO papers?
Take care
Oliver
On 10/30/07, zuc...@research.dfci.harvard.e du

Re: Meeting today

2007-10-30T11:59:51Z

Hi Oliver,
We will meet on Tuesday Oct 30th from 3-5 in Stata 346. See a previous
message for directions.
Agenda:
Organization & goals
OWL exercises
BFO papers
LSW questions & demonstrations
Time permitting, convert Michel's ontology
Sincerely,
Jeremy

Meeting today

2007-10-30T11:18:35Z

Dear friends,
Where are we meeting today? Same room as last time?
Anything particular on the agenda?
Take care
Oliver

SPARQL Query Over Distributed Heterogeneous Data - INVITATION TO PRODUCT LAUNCH

2007-10-25T00:22:58Z

Hi all
I believe some of you participating here will be interested in this..
The Semantic Discovery System V7 Releases 0 & 1
Providing Optimally Performing SPARQL Access Over Multiple Distributed
And Heterogeneous Data Sources
A web based copy of the intro email I would send is here:
[link]

Re: Unifying KEGG and BioCyc with InChI's

2007-10-16T00:43:01Z

Cool!
Grrr... now i wanna get out of my department meeting on Wed ;-)
Let me know what i can do to help.
-=Michel=-
On 10/15/07, zuc...@research.dfci.harvard.e du <

Unifying KEGG and BioCyc with InChI's

2007-10-15T21:46:40Z

Hey Michel,
I am inspired by your enthusiasm, and I think that unifying KEGG and
BioCyc compounds would be an excellent use case for us, enabling real
data integration to motivate our BioPAX representation. I spoke with
Peter Karp about this possibility on Friday, and I will be at SRI on
Thursday where we can discuss this further. He may be able to provide

BioPAX-Boston meeting Wed 17 October 2007

2007-10-15T17:13:12Z

Wednesday, 3-5. Agenda: More about how one would recast BioPAX using
the methods of the OBO Foundry.
We'll be in Stata 346 this time. Why the change? Because it's closer
to my office than our room last week.
Location is directly below last week's room: 3rd floor, Gates (i.e.
east/Main St) tower. From the elevator go right, through doors, left,

What BioPAX communicates and how to extend OWL to help it (was: BioPAX Boston meeting, 11 October 2007)

2007-10-12T16:26:39Z

Dear friends,
I think the paper accurately describes the tensions surrounding
BioPAX and I like the proposals to extend OWL with one caveat: I would
not propose them as extensions of OWL, but as a separate layer.
The extensions are very useful and easily implemented in principle,
but deeply clash with OWL principles. As the authors understand, they

Re: meeting today

2007-10-12T13:40:37Z

Alan, Jeremy
Thanks! What a great analysis! Well substantiated.
So, is it worthwhile to scan through the pathway/reaction databases and
enumerate which identifiers are being used?
-=Michel=-
On 10/12/07, zuc...@research.dfci.harvard.e du <

Re: meeting today

2007-10-12T11:22:34Z

Are you in town now?
Joanne Luciano, PhD
Predictive Medicine, Inc.
45 Orchard Street
Belmont MA 02478-3008
Email: jluci...@predmed.com

Re: meeting today

2007-10-12T08:22:01Z

I sent off the last email before finishing the analysis:
5. IUPAC matching: synonyms are still the way that humans match
compounds. it is possible to take an IUPAC name and uniquely identify the
structure, but not the other way around.
[link]

Re: meeting today

2007-10-12T07:59:12Z

Hey Michel,
Sure. Glucose is a good example.
In the representation suggested by Alan, we should consider all
molecules as classes that are represented to some degree of
specification.
There are several choices for trying to reconcile compounds in different
databases.
In Reactome,
1. unify by Xref. If both compounds have the same KEGG ID, CHEBI ID, CAS

Re: meeting today

2007-10-12T06:44:35Z

I agree that this is a challenge. (Glucose is a particularly nasty
case, as it happens)
In cases where both database providers have provided what are
intended as unification xrefs to a third database, and there is an
entity in each that identifies using the same third party, we can
hypothesize that they are the same. This may turn out to be correct